Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process.
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The aminoacyl-tRNA synthetases (AARSs) and their relationship to the genetic code are examined from the evolutionary perspective. Despite a loose correlation between codon assignments and AARS evolutionary relationships, the code is far too highly structured to have been ordered merely through the evolutionary wanderings of these enzymes. Nevertheless, the AARSs are very informative about the evolutionary process. Examination of the phylogenetic trees for each of the AARSs reveals the following. (i) Their evolutionary relationships mostly conform to established organismal phylogeny: a strong distinction exists between bacterial- and archaeal-type AARSs. (ii) Although the evolutionary profiles of the individual AARSs might be expected to be similar in general respects, they are not. It is argued that these differences in profiles reflect the stages in the evolutionary process when the taxonomic distributions of the individual AARSs became fixed, not the nature of the individual enzymes. (iii) Horizontal transfer of AARS genes between Bacteria and Archaea is asymmetric: transfer of archaeal AARSs to the Bacteria is more prevalent than the reverse, which is seen only for the "gemini group. " (iv) The most far-ranging transfers of AARS genes have tended to occur in the distant evolutionary past, before or during formation of the primary organismal domains. These findings are also used to refine the theory that at the evolutionary stage represented by the root of the universal phylogenetic tree, cells were far more primitive than their modern counterparts and thus exchanged genetic material in far less restricted ways, in effect evolving in a communal sense. (+info)
Spirochaeta aurantia has diacetyl chloramphenicol esterase activity.
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The free-living spirochete Spirochaeta aurantia was nearly as susceptible to diacetyl chloramphenicol, the product of chloramphenicol acetyltransferase, as it was to chloramphenicol itself. This unexpected susceptibility to diacetyl chloramphenicol was wholly or partly the consequence of intrinsic carboxylesterase activity, as indicated by high-performance liquid chromatography, thin-layer chromatography, and microbiological assays. The esterase converted the diacetate to chloramphenicol, thus inhibiting spirochete growth. The esterase activity was cell associated, reduced by proteinase K, eliminated by boiling, and independent of the presence of either chloramphenicol or diacetyl chloramphenicol. S. aurantia extracts also hydrolyzed other esterase substrates, and two of these, alpha-napthyl acetate and 4-methylumbelliferyl acetate, identified an esterase of approximately 75 kDa in a nondenaturing gel. Carboxylesterases occur in Streptomyces species, but in this study their activity was weaker than that of S. aurantia. The S. aurantia esterase could reduce the effectiveness of cat as either a selectable marker or a reporter gene in this species. (+info)
Characterization of a novel spirochete associated with the hydrothermal vent polychaete annelid, Alvinella pompejana.
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A highly integrated, morphologically diverse bacterial community is associated with the dorsal surface of Alvinella pompejana, a polychaetous annelid that inhabits active high-temperature deep-sea hydrothermal vent sites along the East Pacific Rise (EPR). Analysis of a previously prepared bacterial 16S ribosomal DNA (rDNA) library identified a spirochete most closely related to an endosymbiont of the oligochete Olavius loisae. This spirochete phylotype (spirochete A) comprised only 2.2% of the 16S rDNA clone library but appeared to be much more dominant when the same sample was analyzed by denaturing gradient gel electrophoresis (DGGE) and the terminal restriction fragment length polymorphism procedure (12 to 18%). PCR amplification of the community with spirochete-specific primers used in conjunction with DGGE analysis identified two spirochete phylotypes. The first spirochete was identical to spirochete A but was present in only one A. pompejana specimen. The second spirochete (spirochete B) was 84.5% similar to spirochete A and, more interestingly, was present in the epibiont communities of all of the A. pompejana specimens sampled throughout the geographic range of the worm (13 degrees N to 32 degrees S along the EPR). The sequence variation of the spirochete B phylotype was less than 3% for the range of A. pompejana specimens tested, suggesting that a single spirochete species was present in the A. pompejana epibiotic community. Additional analysis of the environments surrounding the worm revealed that spirochetes are a ubiquitous component of high-temperature vents and may play an important role in this unique ecosystem. (+info)
Nitrogen fixation by symbiotic and free-living spirochetes.
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Spirochetes from termite hindguts and freshwater sediments possessed homologs of a nitrogenase gene (nifH) and exhibited nitrogenase activity, a previously unrecognized metabolic capability in spirochetes. Fixation of 15-dinitrogen was demonstrated with termite gut Treponema ZAS-9 and free-living Spirochaeta aurantia. Homologs of nifH were also present in human oral and bovine ruminal treponemes. Results implicate spirochetes in the nitrogen nutrition of termites, whose food is typically low in nitrogen, and in global nitrogen cycling. These results also proffer spirochetes as a likely origin of certain nifHs observed in termite guts and other environments that were not previously attributable to known microbes. (+info)
Carotenoid pigments of facultatively anaerobic spirochetes.
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Carotenoid pigments were purified from a previously undescribed, red, halophilic spirochete (spirochete RS1), and from Spirochaeta aurantia strain J1. Both spirochetes are facultative anaerobes and produce pigments when growing aerobically. The major pigments of the two spirochetes were identified by means of chromatographic analysis, absorption spectroscopy, hydride reduction, acetylation and silylation experiments, and mass spectrometry. It was concluded that the major pigment from spirochete RS1 was 4-keto-1',2'-dihydro-1'-hydroxytorulene. This conclusion was further supported by infrared spectroscopy and additional analytical data. The evidence showed that the major pigment from S. aurantia was 1',2'-dihydro-1'-hydroxytorulene. Chromatographic and spectrophotometric evidence indicated that this pigment was also present, as a minor carotenoid component, in spirochete RS1. These pigments have been previously detected almost exclusively in gliding bacteria, such as species of Flexibacter, Stigmatella, and Myxococcus. The occurrence of 4-keto-1',2'-dihydro-1'-hydroxytorulene and 1',2'-dihydro-1'-hydroxytorulene in both spirochetes and gliding bacteria may have significance with respect to the evolutionary development of these organisms. (+info)
Synergism between Trichuris suis and the microbial flora of the large intestine causing dysentery in pigs.
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The role of the microbial flora of the large intestine in experimental Trichuris suis infection was studied by comparing the clinical syndrome in conventionally reared (CR) pigs, specific pathogen-free pigs, and gnotobiotic pigs. Thedisease in CR pigs was characterized by a severe mucohemorrhagic enteritis; in contrast, a mild catarrhal enteritis was observed in specific pathogen-free and gnotobiotic pigs. Spirochaetes and vibrio-like organisms were observed only in CR pigs and increased during the clinical phase of the disease. The clinical syndrome was not transmitted by oral administration of intestinal or fecal material from infected CR pigs to CR pigs free of T. suis. Smaller numbers of T. suis produced diarrhea in CR pigs and significantly reduced the growth rates of infected animals; clinical signs and the reduction in growth rate was prevented by incorporating an antibacterial substance (dimetridazole) in the food. Although clinical trichuriasis closely resembles swin dysentery, the two syndromes seem to be distinct. The present results suggest that a microbial component acts synergistically with T. suis to produce the severe clinical syndrome in CR pigs, but identification of the microbial component and the mechanism by which clinical signs are produced await further studies of the bacterial flora of the large intestine of pigs. (+info)
Carriage of intestinal spirochaetes by humans: epidemiological data from Western Australia.
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The purpose of this study was to investigate carriage of intestinal spirochaetes by selected population groups in Western Australia. Stool specimens from 293 rural patients with gastrointestinal disorders, and from 227 healthy migrants from developing countries were cultured. Spirochaete isolates were identified using PCR, and typed by pulsed field gel electrophoresis (PFGE). Brachyspira aalborgi was not isolated. Brachyspira pilosicoli was recovered from 15 rural patients, all Aboriginal. Prevalence was 9.9% in 151 Aboriginals and 0% in 142 non-Aboriginals. Carriage of B. pilosicoli amongst migrants was 10.6% (24/227). Carriage was significantly increased in Aboriginal children aged 2-5 years (P = 0.0027) and in migrant individuals from the Middle East and Africa (P = 0.0034). Carriage was significantly associated with detection of faecal protozoa in both Aboriginals (P = 0.0021) and migrants (P = 0.012). PFGE results indicated that the B. pilosicoli strains were genetically diverse. (+info)
Evolutionary implications of microbial genome tetranucleotide frequency biases.
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We compared nucleotide usage pattern conservation for related prokaryotes by examining the representation of DNA tetranucleotide combinations in 27 representative microbial genomes. For each of the organisms studied, tetranucleotide usage departures from expectations (TUD) were shared between related organisms using both Markov chain analysis and a zero-order Markov method. Individual strains, multiple chromosomes, plasmids, and bacteriophages share TUDs within a species. TUDs varied between coding and noncoding DNA. Grouping prokaryotes based on TUD profiles resulted in relationships with important differences from those based on 16S rRNA phylogenies, which may reflect unequal rates of evolution of nucleotide usage patterns following divergence of particular organisms from a common ancestor. By both symmetrical tree distance and likelihood analysis, phylogenetic trees based on TUD profiles demonstrate a level of congruence with 16S rRNA trees similar to that of both RpoA and RecA trees. Congruence of these trees indicates that there exists phylogenetic signal in TUD patterns, most prominent in coding region DNA. Because relationships demonstrated in TUD-based analyses utilize whole genomes, they should be considered complementary to phylogenies based on single genetic elements, such as 16S rRNA. (+info)